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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgacaattcttcatcttgagttaaattaataatggttgatgagcctacatcatctgaagacaagattcatgtatcaacatgttgctttcagacagTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGGAAAGTTGCTACTCCTGAGCAAGCTCAGGAAGTTCATGCT

Basic information

species Oryza sativa
transcript LOC_Os09g36450.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g36450.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G852968_T02 (Zea mays), 3'ss of exon 6
gtgacaattcttcatcttgag-ttaaattaataatggtt-----gatgagccta-----catcatctgaagacaagat--tcatgtat---caacatgt---tgctttcagacagTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGGAAAGTTGCTACTCCTGAGCAAGCTCAGGAAGTTCATGCT
|||| | |||||||||||  | ||   || ||    |||     || ||   |      |||    | |     || |  | ||| ||   ||||||||   ||||| |||| |||||| |||||||||| ||||| || ||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||| |||||||||||    
gtgaaatttcttcatcttaggattttttttatgggcgttctagagaagaagttgggaggcattgatttagcttgaggtgttgatgcatgcgcaacatgtatctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGAAAAGTTGCTACTCCTGAGCAAGCCCAGGAAGTTCA----

upper sequence: LOC_Os09g36450.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G002807_T01 (Zea mays), 3'ss of exon 6
gtgacaatt-cttcatcttgagttaaattaataatgg-----ttgatgagcctaca----------tcatctgaagacaagattcatgtatcaacatgt---tgctttcagacagTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGGAAAGTTGCTACTCCTGAGCAAGCTCAGGAAGTTCATGCT
|||| | || ||||||||| ||  |  ||  || |||     | ||  ||  |  |          | |||||| |    ||| ||| |  ||||||||   ||| | |||| |||||| |||||||||| ||||| ||||||||||| |||||||||||||||||||||||||| ||||||||||||||||| ||||| |||||||||||    
gtgaaactttcttcatcttaagaaacttttttattggcattctagagaagtttgtaggcattgatttaatctgaggtgttgatgcatatg-caacatgtatctgcctgcagATAGTATTTCAAACTGGGCAGATGTTGTAATTGCATACGAGCCTGTTTGGGCTATTGGAACCGGAAAAGTTGCTACTCCTGAACAAGCCCAGGAAGTTCA----

upper sequence: LOC_Os09g36450.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA03G34300.1 (Glycine max), 3'ss of exon 6
------------------gtgacaattcttcatcttgagttaaattaataatggttgatgagcct--acatcatctgaagacaagattcatg-tatcaa-catgt-tgctttcagacagTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGGAAAGTTGCTACTCCTGAGCAAGCTCAGGAAGTTCATGCT
                     |  ||  | ||| |  |||  | ||  |   |    |  |  ||  | |   | ||  ||     | |||   ||| | | ||| ||  | |||||    || | |  ||||   |  | || ||||||||||| ||||| ||||| |||||||| || ||||| || |||||  | |||||||||||||| ||    
gtaggtgcaagctatatttctaatataatccatttaaagtccattttctttggaaaaaacaaactggagagggtttgctgattgcttgcataacatccatcgtgtctgtatgcagACGCAGTTGCTAGTTGGGACAACATTGTTATTGCATATGAACCTGTATGGGCCATTGGAACGGGCAAAGTGGCCACTCCCCAACAAGCTCAGGAAGTACA----

upper sequence: LOC_Os09g36450.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA19G36990.2 (Glycine max), 3'ss of exon 6
-------------------------------gtgacaattcttcatcttgagttaaattaataatggttgatgagcctacatcatctgaagacaagattcatgtatcaacatgttgctttcagacagTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGGAAAGTTGCTACTCCTGAGCAAGCTCAGGAAGTTCATGCT
                                | | ||||| |  ||||   || | |||  |       | | |     ||    ||       |  | |  |         ||  || ||||     || | | |||||   |  | || ||||||||||| ||||| |||||||||||||| || ||||| || |||||  |||||||||||||||| ||    
gtagtggaagttatgtttcttatataatccatttaaaattcgttttctt---ttgatttagaagaaacaaaaggggaaggatttggtggttgattgcattacatcgtttgccattatttacagATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGGCTATTGGAACGGGCAAAGTGGCCACTCCCCAGCAAGCTCAGGAAGTACA----

upper sequence: LOC_Os09g36450.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA10G06740.1 (Glycine max), 3'ss of exon 6
-----gtgacaat--tcttcatcttgagttaaattaataatggttgatgagcctacatcatctgaagacaagatt-catgtatca-acatgttgctttcagacagTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGGAAAGTTGCTACTCCTGAGCAAGCTCAGGAAGTTCATGCT
      ||| | |  | ||| | ||  ||  |   || ||  |  |  | |  |   |   |    ||    ||  |||   | |      ||   | ||||     |  |||  ||||   || |||| ||||||||||||||||| ||||| |||||||| || ||||| || || || |||||||| |||||||| ||    
tttatttgaaagtcattttctttttaggtggagaaaagaaaagaagg-gggagtgggttgccgattgattccataacatcctttatgtccattatatgcagATGTAGTGCCAAGTTGGGATAATATAGTTATTGCATATGAGCCTGTATGGGCAATTGGAACTGGCAAAGTGGCCACACCCGAGCAAGCCCAGGAAGTCCA----

upper sequence: LOC_Os09g36450.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G20930.1 (Glycine max), 3'ss of exon 6
-------gtgacaattcttcatcttgagttaaattaataatggttg-atgagcctacatcatctgaagacaagattcatgtatcaacatgttgctttcagacagTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGGAAAGTTGCTACTCCTGAGCAAGCTCAGGAAGTTCATGCT
       |  |    ||||| | ||  ||  |   || ||| |  | | |||   | | ||  |     | | |      | |       ||   | ||||     |  |||  ||||   || |||| ||||||||||||||||| ||||| |||||||| || ||||| || || || |||||||| |||||||| ||    
ttcattagaaagtcatcttctttttaggtggagaaaagaataggagcaagaggggatagcagattgtttccataacatcctttatgtccattatgtgcagATGCAGTGCCAAGTTGGGATAATATAGTTATTGCATATGAGCCTGTATGGGCAATTGGAACTGGCAAAGTGGCCACACCCGAGCAAGCCCAGGAAGTCCA----

upper sequence: LOC_Os09g36450.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv03s0038g01780.t01 (Vitis vinifera), 3'ss of exon 6
-------------gtgacaat-tcttcatcttgagttaaattaataatggttgatgagcctacatcatctgaa---gacaagattcatgtatcaacatgttgcttt---------cagacagTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGGAAAGTTGCTACTCCTGAGCAAGCTCAGGAAGTTCATGCT
              |||   | ||||  || ||   |  | |     |   || |   | |     |   |||   |   |   |  |||| || |    |  ||          ||||   | |  | |  ||||  |||||||| |||||||||||||| ||||||||||||||||| || ||||| || || ||   ||| || |||||||| ||    
gcaagttctcttgctgatgttctctttctcatggaatgtactgtcgttttgtggtcctcttgtgaaaagagaacttgttgactcttttgtaacatcgctcttgttcaatcatgcgcagATGCTGTACCCAGTTGGGATGATGTAGTTATTGCATATGAGCCGGTTTGGGCTATTGGAACTGGTAAAGTGGCCACACCCCTGCAGGCACAGGAAGTACA----

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|38480252|gb|CF964341.1|CF964341
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         A
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... tttcagacag-
EST: gi|38480252|gb|CF964341.1|CF964341
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         A
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... tttcagacag-
EST: gi|38480252|gb|CF964341.1|CF964341
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         A
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... tttcagacag-
EST: gi|38480252|gb|CF964341.1|CF964341
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         A
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... tttcagacag-
EST: gi|38480252|gb|CF964341.1|CF964341
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         A
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... tttcagacag-
EST: gi|29641345|gb|CB646352.1|CB646352
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGACAG                      
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTT---G-CAGgtgacaattc ... tttcaga
EST: gi|33682001|gb|CF310240.1|CF310240
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         A
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... tttcagacag-
EST: gi|33682001|gb|CF310240.1|CF310240
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         A
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... tttcagacag-
EST: gi|33682001|gb|CF310240.1|CF310240
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         A
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... tttcagacag-
EST: gi|33682001|gb|CF310240.1|CF310240
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         A
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... tttcagacag-
EST: gi|33682001|gb|CF310240.1|CF310240
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         A
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... tttcagacag-
EST: gi|29637218|gb|CB642227.1|CB642227
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGACAG                      
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTT---G-CAGgtgacaattc ... tttcaga
EST: gi|29667622|gb|CB663897.1|CB663897
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         A
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... tttcagacag-
EST: gi|29667622|gb|CB663897.1|CB663897
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         A
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... tttcagacag-
EST: gi|29667622|gb|CB663897.1|CB663897
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         A
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... tttcagacag-
EST: gi|29667622|gb|CB663897.1|CB663897
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         A
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... tttcagacag-
EST: gi|29667622|gb|CB663897.1|CB663897
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         A
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... tttcagacag-
EST: gi|87020131|gb|CI277863.1|CI277863
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAG                         TATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGGCTAT
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaattc ... tttcagacagTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGGCTAT
EST: gi|86902043|gb|CI300282.1|CI300282
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGACAG                      
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTT---G-CAGgtgacaattc ... tttcaga
EST: gi|29645954|gb|CB650961.1|CB650961
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGACAG                      
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTT---G-CAGgtgacaattc ... tttcaga
EST: gi|86505521|gb|CI148154.1|CI148154
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGACAG                      
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTT---G-CAGgtgacaattc ... tttcaga
EST: gi|29678932|gb|CB675207.1|CB675207
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGACAG                      
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTT---G-CAGgtgacaattc ... tttcaga
EST: gi|29638544|gb|CB643553.1|CB643553
EST:     AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGACAG                      
genomic: AGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTT---G-CAGgtgacaattc ... tttcaga


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagcctacatcatctgaagacaagattcatgtatcaacatgttgctttcagacagTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGGAAAGTTGCTACTCCTGAGCAAGCTCAGGAAGTTCATGCT
                                         ttgctttc  CT-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgacaattcttcatcttgagttaaattaataatggttgatgagcctacatcatctgaagacaagattcatgtatcaacatgttgctttcagacagTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGGAAAGTTGCTACTCCTGAGCAAGCTCAGGAAGTTCATGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA